long-read-pipelines
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broadinstitute
Long read production pipelines
This pull requests adds a WDL pipeline and required WDL tasks to review a large number of variants. Candidate variants are called by comparing two high quality references, using Nucmer...
The [preprint](https://www.biorxiv.org/content/10.1101/2021.06.09.447198v1) and the [repo](https://github.com/qm2/NanoSpring), for compressing data, (semi?-) reference free. Also, it's not clear if the same can/cannot be applied to CLR data as well.
I wasn't paying enough attention to hifiasm as I should have, and just realized that hifiasm can do trio-binning too. Though unsure if it'd work on non-HiFi reads (trio-canu does),...
Implement a WDL task and evaluate the use of the noise-cancelling repeat finder (NCRF). From the manuscript (https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz484/5530597): **Abstract** Summary Tandem DNA repeats can be sequenced with long-read technologies, but...
In the PBCCSWholeGenomeSingleFlowcell workflow, in CallSVs, Sniffles task I got an error where it sounds like there's too few reads in the bam to estimate some parameter it needs? Log...
We need to check if the metadata has been uploaded already. Otherwise there will be duplicate rows.
Now that we showed trio-assembly costs can be lowered to sub $10, it makes sense to have a (sub-) pipeline for quality assessment on routine trio-assembly. Currently, I'm experimenting with...
